A new graphical user interface (GUI) for the parsimony program TNT is presented that works
under the Linux and Mac operating systems, as well as the Cygwin environment (which runs …

Abstract Background The Sackin index S of a rooted phylogenetic tree, defined as the sum
of its leaves' depths, is one of the most popular balance indices in phylogenetics, and …

Measures of tree balance play an important role in the analysis of phylogenetic trees. One of
the oldest and most popular indices in this regard is the Colless index for rooted bifurcating …

The shape of phylogenetic trees can be used to gain evolutionary insights. A tree's shape
specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic …

The Colless index for bifurcating phylogenetic trees, introduced by Colless (1982), is defined
as the sum, over all internal nodes v of the tree, of the absolute value of the difference of the …

This paper discusses the problem of whether creating a matrix with all the character state
combinations that have a fixed number of steps (or extra steps) on a given tree T, produces …

Motivation TNT (a widely used program for phylogenetic analysis) includes an interpreter for
a scripting language, but that implementation is nonstandard and uses several conventions …

In this study, we investigate the problem of comparing gene trees reconciled with the same
species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) …

Time trees are evolutionary histories (also called phylogenies) that include times of
evolutionary events. They arise in many applications, including cancer and virus evolution …

[eng] The main motivation behind the quantitative study of phylogenetic tree shapes is the
belief that they reflect properties of the evolutionary processes that have derived them. The …